Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm

Abstract

An iterative transform method proposed previously for direct phasing of highsolvent-content protein crystals is employed for enhancing the molecularreplacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationship of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.

Direct Phasing of Protein Crystals with Non-Crystallographic Symmetry

“…Iterative phasing algorithms have been proposed to solve the phase problem of protein crystallography [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15]. Liu et al showed that direct phasing of protein structures is possible when the protein boundary is known or can be derived from other experiments, such as small-angle X-ray scattering [8].…”

Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography

“…The HIO phasing algorithm has been successfully demonstrated for high-resolution structures [13][14][15]. However, it is not entirely clear that it will yield anything useful when the effective resolution is less than 3 Å.…”

“…Ab initio phasing using the HIO method has been described in previous articles [13][14][15]27,28]. In this paper, we made 200 independent runs for each trial calculation and each run has 10,000 iterations.…”

“…In practice, the weighted average density is calculated in reciprocal space according to the convolution theorem. More information about the calculation of the weighted average density can be found in our previous articles [13,14].…”

“…Despite the existence of good physical methods for phasing the X-ray reflections of a protein crystal, direct phasing remains a challenging theoretical problem. Iterative projection algorithms have been widely used for phase retrieval [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17].…”